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MD5Sums of fastq files from SRA

Hi all,

I downloaded a bunch of fastq files using wget. i.e. wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/072/SRR13198172/SRR13198172.fastq.gz

I did this because SRA download was either failing or taking forever.

I need to verify file integrity with MD5sums. Is there a way to get this information? or extract it from SRA somehow?

thanks!

md5sum fastq sra verify
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updated by ATpoint ATpoint • written by ildem • ildem

2 answers

Tbh I would just download it via the Aspera links. Aspera is smart and only creates the final file if the download finishes successfully, so md5 are not necessary here.

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written by ATpoint ATpoint

Query ENA archive and select sra_md5 as one of the output fields (I think that's what you want). In practice, though, I think that checking the integrity of the gzip file (gzip -t) should give you a pretty good reassurance that the file is complete.

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written by dariober dariober

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